What is a species?

  • No one really knows

Physical barriers lead to isolation

  • Pattern of surface currents in the indonesian islands
  • Isolation eventually leads to speciation
  • Species boundaries in closely related species are often fuzzy
  • It can be hard to distinguish closely related "cryptic" species

Eviota atriventris

  • The Blackbelly dwarf goby
  • A cryptobenthic reef fish
  • Map (right) shows range throughout the tropical Indo-Pacific

Plot twist

  • some E. atriventris don't have a black belly Leads to the question

  • Are they different species?

  • Look for evidence of differentiation by examining external morphology

Pelvic fin morphology data

  • contains individual ID no, sample locality, region (east or west), sex, pelvic fin characters
  • some bad data columns
Specimen DNA. X locality haplotype SL.mm. sex fifth_fourth_ratio pelvic_length membrane_length branches jaw_eye
ROM 92305 no Papua New Guinea east 17.9 male 0.79 3.5 0.75 2 anterior margin of pupil
ROM 92305 no Papua New Guinea east 14.5 male 0.50 4.0 0.75 2 anterior margin of pupil
ROM 92305 no Papua New Guinea east 14.3 male 0.50 NA 0.75 NA anterior margin of pupil
ROM 92309 no Papua New Guinea east 16.2 female 0.50 3.5 0.75 2 middle of pupil
ROM 92309 no Papua New Guinea east 17.6 male NA NA NA NA middle of pupil
ROM 84482 no Palau west 17.9 male 0.50 4.1 0.50 6 middle of pupil (see picture)

Use tidyr to separate specimen identification information

knitr::kable(head(separate(morph, Specimen, c("museum", "jar_no.", 
                                              "id."), sep = " ")))
museum jar_no. id. DNA. X locality haplotype SL.mm. sex fifth_fourth_ratio pelvic_length membrane_length branches jaw_eye
ROM 92305 NA no Papua New Guinea east 17.9 male 0.79 3.5 0.75 2 anterior margin of pupil
ROM 92305 NA no Papua New Guinea east 14.5 male 0.50 4.0 0.75 2 anterior margin of pupil
ROM 92305 NA no Papua New Guinea east 14.3 male 0.50 NA 0.75 NA anterior margin of pupil
ROM 92309 NA no Papua New Guinea east 16.2 female 0.50 3.5 0.75 2 middle of pupil
ROM 92309 NA no Papua New Guinea east 17.6 male NA NA NA NA middle of pupil
ROM 84482 NA no Palau west 17.9 male 0.50 4.1 0.50 6 middle of pupil (see picture)

Comparing branch number between eastern and western populations

  • histograms show no difference between eastern and western morphs

Taking subsets of data to run a t test

  • Compares number of branches on the 4th pelvic ray in eastern vs western groups
west <- filter(morph, haplotype == "west")
east <- filter(morph, haplotype == "east")
## 
##  Welch Two Sample t-test
## 
## data:  west$branches and east$branches
## t = 1.9901, df = 32.815, p-value = 0.05497
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -0.01727863  1.55061196
## sample estimates:
## mean of x mean of y 
##  3.766667  3.000000
  • An insignificant p value (>0.05) suggests no difference

Analyzing all four pelvic characters at once

  • we will use a principal component analysis
  • this loadings data for PC1 and PC2 will be used to make a plot
## 
## Loadings:
##                    Comp.1 Comp.2 Comp.3 Comp.4
## fifth_fourth_ratio  0.558 -0.159  0.738  0.346
## pelvic_ratio       -0.556  0.219  0.672 -0.437
## fin_membrane        0.596  0.102        -0.794
## branches           -0.157 -0.957        -0.242
## 
##                Comp.1 Comp.2 Comp.3 Comp.4
## SS loadings      1.00   1.00   1.00   1.00
## Proportion Var   0.25   0.25   0.25   0.25
## Cumulative Var   0.25   0.50   0.75   1.00

PCA Plot

  • shows high overlap and no difference between groups

Synthesis

  • it is interesting that there is no morphological difference

  • but there are genetic differences

  • It is hard to tell if they are separate species, since some evidence suggests separation but a taxonomist would use this morphological analysis to argue that they are the same